A number of small hospitals have been identified as not having safe and sustainable measures in place to protect patients from superbugs.
A report by the Health Information and Quality Authority has found "this is a significant patient safety concern".
HIQA has urged the HSE to review the situation "as a matter of urgency".
The discovery of antimicrobial agents, such as penicillin, were a major triumph in medicine. But resistance to these drugs is now growing, meaning that more highly resistance infections are emerging.
The rates of MRSA and Clostridium difficile have fallen in Ireland.
However, resistance to other bacteria associated with serious infections, such as life-threatening sepsis, is increasing.
HIQA has examined how public acute hospitals are dealing with the threat.
It found that while many hospitals have made significant progress to protect patients from superbugs, more needs to be done in smaller hospitals, and in non-acute settings such as nursing homes.
